7Z5Y

CRYSTAL STRUCTURE OF WEISSELLA VIRIDESCENS FEMXVV NON-RIBOSOMAL AMINO ACID TRANSFERASE IN COMPLEX WITH A PEPTIDYL-XNA CONJUGATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 

Starting Model: experimental
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This is version 2.3 of the entry. See complete history


Literature

Amino-acyl tXNA as inhibitors or amino acid donors in peptide synthesis.

Rietmeyer, L.Li De La Sierra-Gallay, I.Schepers, G.Dorchene, D.Iannazzo, L.Patin, D.Touze, T.van Tilbeurgh, H.Herdewijn, P.Etheve-Quelquejeu, M.Fonvielle, M.

(2022) Nucleic Acids Res 50: 11415-11425

  • DOI: https://doi.org/10.1093/nar/gkac1023
  • Primary Citation of Related Structures:  
    7Z5Y, 7Z5Z, 7Z6A, 7Z6K

  • PubMed Abstract: 

    Xenobiotic nucleic acids (XNAs) offer tremendous potential for synthetic biology, biotechnology, and molecular medicine but their ability to mimic nucleic acids still needs to be explored. Here, to study the ability of XNA oligonucleotides to mimic tRNA, we synthesized three L-Ala-tXNAs analogs. These molecules were used in a non-ribosomal peptide synthesis involving a bacterial Fem transferase. We compared the ability of this enzyme to use amino-acyl tXNAs containing 1',5'-anhydrohexitol (HNA), 2'-fluoro ribose (2'F-RNA) and 2'-fluoro arabinose. L-Ala-tXNA containing HNA or 2'F-RNA were substrates of the Fem enzyme. The synthesis of peptidyl-XNA and the resolution of their structures in complex with the enzyme show the impact of the XNA on protein binding. For the first time we describe functional tXNA in an in vitro assay. These results invite to test tXNA also as substitute for tRNA in translation.


  • Organizational Affiliation

    INSERM UMR-S 1138, Centre de Recherche des Cordeliers, Sorbonne Université, Université Paris Cité, F-75006 Paris, France.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UDP-N-acetylmuramoylpentapeptide-lysine N(6)-alanyltransferase343Weissella viridescensMutation(s): 0 
Gene Names: femX
EC: 2.3.2.10
UniProt
Find proteins for Q9EY50 (Weissella viridescens)
Explore Q9EY50 
Go to UniProtKB:  Q9EY50
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9EY50
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
UDP-MurNAc-pentapeptide5synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
HNA (5'-D(P*(6HA)P*(6HC)P*(6HC))-R(P*(A9Z))-3')4synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.16α = 90
b = 101.96β = 102.78
c = 46.19γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French Infrastructure for Integrated Structural Biology (FRISBI)FranceANR-10-INBS-05

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-26
    Type: Initial release
  • Version 1.1: 2022-11-23
    Changes: Database references
  • Version 2.0: 2022-12-07
    Changes: Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2022-12-14
    Changes: Database references
  • Version 2.2: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 2.3: 2024-10-09
    Changes: Structure summary